Tag: Matthew Herper

Food for Thought: Weekly Wrap-Up

The EHEC epidemic in Germany with 4,300 patients and 50 deaths has changed the way public health institutions will deal with future epidemics, writes Christina Hucklenbroich in Frankfurter Allgemeine Zeitung (FAZ). She cites microbiologists involved in the rapid sequencing of the EHEC strain who think that the epidemic gave birth to the new discipline of “prospective genomic epidemiology”. To date, sequencing has been performed retrospectively only. However, using the novel Ion Torrent PGM HGS platform, scientists from the University of Münster were able to sequence the EHEC strain responsible for the outbreak within 62 hours. The scientists now think of a software generating a plain language report interpreting the genome and analyzing for toxins and antibiotics resistances of the germ in question so that immediate therapeutic and prophylactic consequences are possible.

Gas, electricity and hydrogen from algae are in the focus of a story by Susanne Kutter in Wirtschaftswoche. She features Sven Kerzenmacher and Johannes Gescher from the University of Freiburg and their efforts to produce electrical current directly from bacteria. The technology is based on the Shewanella bacterium which can transfer electrons generated by breakdown of sugar or other nutrients from the cell surface to conductive materials. Shewanella lives in fresh-, brack- and seawater and thrives on organic waste. The researchers are now trying to design a Shewanella-based mini-powerplant the size of a refrigerator which is able to produce 5-10 Watts of electricity per day – sufficient to meet the demand of a four-person household. Among others, Kutter also features a dual-chamber solar module developed by researchers from Leipzig, Karlsruhe and Bremen. In the first chamber, algae are forced by an excess of oxygen to produce hydrocarbons (“photorespiration”). The hydrocarbons enter the second chamber via a membrane and are used by bacteria to produce methane under anaerobic conditions. Readers interested in learning more about Shewanella may find regular updates on Shewanella Blogger.

While algae seem to be an ideal biofuel replacement for gasoline in the first place, it has turned out that the economics is a problem, writes Erica Gies in Forbes. Gies revisits former biofuel-from-algae startups that are now turning to more profitable products, using “green” chemistry to replace petrochemicals or unsustainable bio-based oils.

Also in Forbes, Matthew Herper deals with an op-ed in Nature Reviews Drug Discovery by John L. LaMattina, ex-CEO of Pfizer, Inc. LaMattina writes the pharma’s M&A activities have had a “devastating” effect of research and development efforts which will impact the industry over the next decade. The comment is all the more telling as LaMattina was pivotal in Pfizer’s acquisitions of Warner-Lambert, Pharmacia, Wyeth and many other companies. LaMattina summarizes that the consolidation by M&A led to fewer companies pursuing novel ideas and disruptions in research processes. Friction is caused, among others, by the need to streamline computer systems, procedures to track side-effects and others. Usually, a merger delays the start of any new research project by nine months. LaMattina’s comment can be accessed here.

Brandon Keim in Wired explains that most genetic differences in people are not caused by mutations but by variations in the genome’s architecture. At present, sequencing is designed to identify SNPs and as every sequencing method is breaking down the DNA in smaller pieces most genomic studies a blind to larger variations. First sequencing studies looking at larger DNA pieces now revealed that individuals seem to be distinguished less by their SNPs than by their structural variations, i.e. wholesale duplications and reversals, or unexpected additions and omissions of long DNA sequences.

Finally, Catherine de Lange in the New Scientist features the first car plugging into the driver’s brain to cut response times in case the car needs to stop suddenly. The invention of Stefan Haufe from the Berlin Institute of Technology uses an EEG headset and sensors on the leg to detect neuronal patterns and muscle tension to find out that the driver intends to apply the brakes. The system improves response times by 130 milliseconds which translates into the length of a small car when stopping from a speed of 100 km/h.

Food for Thought: Weekly Wrap-Up

In Frankfurter Allgemeine Zeitung (FAZ), Manfred Lindinger reports on progress in designing intelligent materials. Physicists of Technical University Hamburg-Harburg succeeded in designing gold- and platinum-based materials that can be switched between hard and brittle or soft and elastic, just by applying different voltages. The trick is done by etching pores and channels into the material which subsequently are filled with perchloric acid.

Martina Lenzen-Schulte, also in FAZ, deals with the surprising finding that a screening test for ovarian cancer increases the number cases detected but at the same time does not improve survival. The test based on the CA-125 tumor marker was investigated in the PLCO longitudinal analysis comprising more than 75,000 women aged between 55 and 74 years, who were diagnosed as cancer-free at the beginning of the study. Half of them was tested once a year with the CA-125 test. While more women were diagnosed with ovarian cancer in the CA-125 test group, the outcome did not improve – in part, because the test did not detect the cancer early enough. Moreover, it resulted in a high number of false positives, and these patients were put at unnecessary risk of bleeding, infections, colon injuries and blood loss due to attempts to confirm the diagnosis via biopsies.

In Forbes, Matthew Herper features an interview with David Urdal, the now retiring CSO of Dendreon, who pioneered Provenge, the prostate cancer vaccine approved by the FDA last year as the first anti-cancer vaccine ever. Urdal in detail explains why the company did not specify overall survival as primary endpoint but choose to follow every patient for three years instead. While the FDA first ok’ed the approach and the FDA advisory committee recommended approval in 2007, the FDA did not approve it: in the committee, cell therapists were in favor of Provenge while the oncologists had doubts. The drug was approved only after another study, the famous IMPACT study, had been finished. Urdal maintains that this turned out to be very positive for Provenge: the study revealed new insights about progression in asymptomatic patients and demonstrated that the method to measure disease progression just by counting the time to the next progression event was inadequate. Urdal states that the FDA may have been right to reject Provenge in the first place: “I think if you follow the sentiments within the clinical community I think there was a sense of, okay, if it’s approved I’d probably prescribe it, but geez, it’s a small study, overall survival wasn’t the primary endpoint, there wasn’t a sense of enthusiasm for it, and I think in the end of course the IMPACT study results came back and this completely vindicated the results from the earlier trials.”

William Pentland, also in Forbes, introduces a new battery architecture invented by the Massachusetts Institute of Technology MIT. The semi-solid flow cell basically runs on “sludge”, combining the structure of so-called flow batteries, where the electrolytes are replaced from outside once they are consumed with the favorable energy potential of lithium-ion batteries. Pentland says the new design may have the potential of a game-changer, in particular in combination with electric cars and smart grids.

Todd Woody, also in Forbes, describes buildings that clean up after itself via panels coated with titanium dioxide particles that serve as photocatalysts. Once illuminated by the sun, the particles start destroying dirt on the panel’s surface and, as a side effect, can also clear the surrounding air from nitrogen oxide. The company selling the panels claims they can cut a building’s maintenance costs by a third to half.

The Economist this week makes a case for using personalized medicine approaches in clinical trials earlier. In most cases, the Economist writes, oncologists “base their treatment on where in the body a tumour has sprung up, rather than on which molecular aberrations have caused it”, adding that the same is true for recruiting volunteers for clinical trials, in particular Phase I.

Drawing conclusions from this year’s ASCO (American Society of Clinical Oncology) meeting, the Economist argues it may be much better to match the genetic profiles of patients to the drug being tested, rather than looking for the organs affected. The magazine introduces a study  by Apostolia-Maria Tsimberidou of the University of Texas’s MD Anderson Cancer Centre, in which the author selected volunteers with late-stage cancer across various organs whose tumors were caused by a single, known mutation. 175 volunteers were administered a targeted therapy in a low-dose, Phase I setting while 116 received traditional therapy. In the targeted therapy group, 29% responded, while in the untargeted therapy group there were only 5% responders.

Mark Brown in Wired reports on Harvard University researchers who created the first living laser, a human embryonic kidney cell that was genetically engineered to produce a visible laser beam. The cell producing green fluorescent protein was put between two mirrors and when the team ran pulses of blue light through the cell, it began to emit green light. When bouncing between the mirrors, certain wavelengths were preferentially amplified until a visible laser beam was created for a few nanoseconds. The cell was left unharmed. At present, researchers foresee applications in cell biology research.

Last not least, Herbert Renz-Polster in Der Spiegel this week answers crucial questions on why  kids like jelly babies buth not salad and Brussels sprouts and how they can be made to eat healthy. The answer: it’s the evolution stupid! It is more advisable to eat fat in order to survive the next famine, to eat hastily (who knows when the next rival appears) and it is also wise to avoid eating the unknown (maybe it’s poison). The simple advice: be patient, keep offering the healthy stuff and play while having a meal. That way, kids even learn to like seal fat, whale blubber and roasted locusts.

Food for Thought: Weekly Wrap-Up

This week, Frankfurter Allgemeine Zeitung (FAZ) deals with potential origins of the enterohemorrhagic E. coli (EHEC) epidemic in Germany. Christina Hucklenbroich details the consequences of feeding cattle mixed provender, a forage that changes the environment of the intestinal tract so that it becomes an ideal habitat for bacteria like E. coli. In a separate article the same author deals with an EHEC outbreak in 1997 in the US which affected mostly women – similar to the current epidemic in Germany. Back then, the source had been alfalfa sprouts used in salads. While the ultimate source had never been found, scientists suspected that already the seeds had been contaminated. Richard Friebe, also in FAZ, deals with slurry from pigs, cattle, and fowl that is know to contain all sorts of bacteria and viruses. It is used either directly as fertilizer (though not on vegetables and salad plants) or may contaminate adjacent fields through spillover, spray or via irrigation using water contaminated with slurry.

Susanne Kutter in Wirtschaftswoche introduces Holger Zinke, co-founder and CEO of BRAIN AG, a biotech company specialized on “white” biotechnology, using the skills of microbes to re-design industrial processes or to come up with entirely new ones. Thereby, pharma and chemical industry can save energy, money, and expenses for raw materials. The article is part of a series on pioneers of the “greentech-era”, trying to change the industry to make it more energy-efficient and sustainable.

In Forbes, Matthew Herper analyses why scientists in Germany and China used small desktop sequencers by Ion Torrent rather than big machines by Illumina, Life or 454 Life Sciences to decipher the sequence of the EHEC strain rampaging through Germany. Herper claims it is speed and cost. However, the choice was also influenced by the fact that the sequence of the new strain matched strains with sequences available in public databases relatively closely so that puzzling together the short sequence data generated by the machine was easy.

In reporting on this year’s annual conference of the American Society of Clinical Oncology (ASCO), Andrew Pollack in The New York Times (NYT) introduces two drugs for the treatment of melanoma: vemurafenib (developed by Genentech, part of Roche Group), which attacks a specific mutation accelerating tumor growth and Yervoi ipilimumab (developed by Bristol-Myers Squibb), which unleashes the body’s immune system to fight the cancer. Yervoi was approved by FDA in March this year. Pollack also features latest clinical results for Aromasin exemestane, a drug marketed for preventing recurrences of breast cancer.

Gina Kolata, also in NYT, deals with the phenomenon of “linguistic toxicity”, i.e. drug labels listing more and more side effects, even contradictory ones such as that a medication can cause diarrhea or constipation. As of today, drug labels in the US list an average of 94 side effects (the top numbers already are exceeding 500), despite efforts of FDA to make drug makers avoid listing of side effects that are infrequent and minor, commonly observed in the absence of drug therapy or not plausibly related to drug therapy. Main reason is pharma companies trying to protect themselves against lawsuits.

Last not least, New Scientist features the latest advice for those of you on diet: psychologist found that if you succeed convincing yourself that everything you eat bears enormous amounts of calories, your ghrelin hormone level will drop much lower after eating so that you feel being full faster.

Food for Thought: Weekly Wrap-Up

Joachim Müller-Jung in Frankfurter Allgemeine Zeitung (FAZ) reports on the rapid spread of infections with enterohemorrhagic Escherichia coli (EHEC) in Germany. In about 20-25% of cases, the disease leads to the life-threatening hemolytic uremic syndrome (HUS) associated with kidney failure. Jung reports about promising treatment strategies using Soliris eculizumab. The monoclonal antibody by Alexion Pharmaceuticals has been approved in the US and the EU in 2007 for the treatment of paroxysmal nocturnal hemoglobinuria.

Also in FAZ, Nicola von Lutterotti features results from molecular psychiatry studies in children brought up in orphanages and adults suffering from trauma. Results demonstrate that there is a strong association between length of stay in an orphanage and factors like learning ability as well as length of telomers. Adults suffering severe trauma during childhood also have significantly shorter telomers.

In Focus, Monika Preuk reports on instant dental implants for diabetics, osteoporosis patients and smokers. These patients often cannot undergo conventional implantation procedures that need careful planning and complex steps of building bone material, placement of titanium posts and periods of long healing times. The new method involves skewed planting of very long implants into the healthy parts of the jawbones. The method stabilizes the jawbone so that implants can be planted within a day.

Matthew Herper in Forbes introduces the 25 most innovative countries in biology and medicine based on data provided by SciVal analytics, an Elsevier division. The complex analysis is based on publications output, number of citations, etc. Still the US dominates the fields, and papers by US scientists are more likely to be cited by other researchers than those in any country – except the Netherlands and Switzerland.

Andrew Pollack in the New York Times introduces Sherwood L. Gorbach, a researcher who helped to develop Dificid, a novel antibiotic against severe diarrheas. The drug by Optimer Pharmaceuticals has just been approved by FDA for the treatment of Clostridium difficile-associated diarrhea.

The Economist features new attempts to vaccinate people against drug abuse. The challenging task is to develop an effective vaccine against  really small and therefore very flexible molecules. A new trick applied for the design of a metamphetamine vaccine uses computer models to design haptens mimicking various metamphetamine-shapes and using these haptens to generate antibodies. Already it has been possible to generate efficacious metamphetamine-antibodies in mice with this method.

And finally, Die Zeit this week deals with the question whether mosquitos get drunk upon sucking blood from drunk people. The answer to the question is that after the blood meal, the mosquitos have about half the blood alcohol concentration of their victim. However, it is unclear whether they show behavioral deficits thereafter. 😉

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